SAXSdb — 1b85

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1. Protein Identity and Related Structures Protein Identity & Related Structures

Ligninase H8

Phanerochaete chrysosporium

State in the Current Structure

Assembly	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain A； UniProt 22–372	Fragment：MATURE PROTEIN PLUS 7-RESIDUE PROSEQUENCE Mutation：W171F SUBSTITUTION	CA CALCIUM ION × 2 HEM PROTOPORPHYRIN IX CONTAINING FE × 1	X-RAY DIFFRACTION X-ray crystallization conditions：pH 4；pH 4.0	Resolution 1.85 Å R-free 0.181
2	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain B； UniProt 22–372	Fragment：MATURE PROTEIN PLUS 7-RESIDUE PROSEQUENCE Mutation：W171F SUBSTITUTION	CA CALCIUM ION × 2 HEM PROTOPORPHYRIN IX CONTAINING FE × 1	X-RAY DIFFRACTION X-ray crystallization conditions：pH 4；pH 4.0	Resolution 1.85 Å R-free 0.181

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB	Difference from Current Entry 1B85	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1B80 REC. LIGNIN PEROXIDASE H8 OXIDATIVELY PROCESSED Deposited 1999-02-03	Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 22–372（351 aa） Fragment：MATURE PROTEIN PLUS 7-RESIDUE PROSEQUENCE	Non-standard monomer：Yes (specific site not provided by mmCIF)	CA CALCIUM ION × 2 HEM PROTOPORPHYRIN IX CONTAINING FE × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 3.5；17 % PEG 6000 PH 3.5	Resolution 1.73 Å R-free 0.208
1B80 REC. LIGNIN PEROXIDASE H8 OXIDATIVELY PROCESSED Deposited 1999-02-03	Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 28–372（345 aa） Fragment：MATURE PROTEIN PLUS 7-RESIDUE PROSEQUENCE	Non-standard monomer：Yes (specific site not provided by mmCIF)	CA CALCIUM ION × 2 HEM PROTOPORPHYRIN IX CONTAINING FE × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 3.5；17 % PEG 6000 PH 3.5	Resolution 1.73 Å R-free 0.208
1B82 PRISTINE RECOMB. LIGNIN PEROXIDASE H8 Deposited 1999-02-04	Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 24–373（350 aa） Fragment：MATURE PROTEIN PLUS 7-RESIDUE PROSEQUENCE	Not recorded	CA CALCIUM ION × 2 HEM PROTOPORPHYRIN IX CONTAINING FE × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 3.5；pH 3.5	Resolution 1.80 Å R-free 0.194
1B82 PRISTINE RECOMB. LIGNIN PEROXIDASE H8 Deposited 1999-02-04	Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 24–373（350 aa） Fragment：MATURE PROTEIN PLUS 7-RESIDUE PROSEQUENCE	Not recorded	CA CALCIUM ION × 2 HEM PROTOPORPHYRIN IX CONTAINING FE × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 3.5；pH 3.5	Resolution 1.80 Å R-free 0.194
6A6Q Crystal structure of a lignin peroxidase isozyme H8 variant that is stable at very acidic pH Deposited 2018-06-29	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 22–372（351 aa）	Mutation：A55R, N156E, H239E Non-standard monomer：Yes (specific site not provided by mmCIF)	HEB HEME B/C × 1 CA CALCIUM ION × 2 GOL GLYCEROL × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5；293 K；PEG 6000	Resolution 1.67 Å R-free 0.171
6ISS Lignin peroxidase H8 triple mutant S49C/A67C/H239 Deposited 2018-11-19	Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 22–372（351 aa）	Mutation：S49C,A67C,H239E Non-standard monomer：Yes (specific site not provided by mmCIF)	HEM PROTOPORPHYRIN IX CONTAINING FE × 1 CA CALCIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；PEG 6000	Resolution 1.53 Å R-free 0.196
6ISS Lignin peroxidase H8 triple mutant S49C/A67C/H239 Deposited 2018-11-19	Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain G 22–372（351 aa）	Mutation：S49C,A67C,H239E Non-standard monomer：Yes (specific site not provided by mmCIF)	HEM PROTOPORPHYRIN IX CONTAINING FE × 1 CA CALCIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；PEG 6000	Resolution 1.53 Å R-free 0.196

4 other PDB entries and 7 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	LIG8_PHACH
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–351； UniProt 22–372 Author chain B； PDBConstruct 1–351； UniProt 22–372

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	1b85
Deposition date deposition_date	1999-02-05
Structure title title	LIGNIN PEROXIDASE
Keywords keywords	;LIGNIN DEGRADATION, HEME, RADICAL REACTION, ELECTRON TRANSFER, OXIDOREDUCTASE, Calcium, Cleavage on pair of basic residues, Disulfide bond, Glycoprotein, Hydrogen peroxide, Iron, Metal-binding, Peroxidase, Zymogen ;; OXIDOREDUCTASE
Experimental Method method	X-RAY DIFFRACTION

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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier	35.53 Å
Radius of gyration Rg (electron density) rg_electron	35.64 Å
Forward intensity I(0) i0	89909500.00
Molecular weight molecular_weight	75320.0 kDa
Excluded volume excluded_volume	93582 Å³
Envelope volume envelope_volume	116420 Å³
Hydration-shell volume shell_volume	29066 Å³
Envelope diameter envelope_diameter	125.7 Å
Shell Rg shell_rg	38.89 Å
Envelope Rg envelope_rg	35.38 Å
Shape Rg shape_rg	35.63 Å
Total Rg total_rg	35.91 Å
Total atoms total_atoms	5300
Residues n_residues	693
Spherical-harmonic order n_harmonics	20
q range q_range	— – 0.5000 Å⁻¹
Data points n_points	101
Shell type shell_type	directional
Solvent electron density solvent_density	0.3340 e/Å³
Shell contrast contrast_shell	0.0300 e/Å³
CRYSOL version crysol_version	4.1.3

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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax	123.5 Å
Rg (real space) rg_real	35.99 Å
Rg uncertainty (real space) rg_real_error	1.08 Å
I(0) (real space) i0_real	8.9910e+07
I(0) uncertainty (real space) i0_real_error	1.3080e+06
Rg (reciprocal space) rg_reciprocal	35.71 Å
I(0) (reciprocal space) i0_reciprocal	89890000.0000
Solution quality estimate total_estimate	0.7240
Solution quality rating solution_quality	REASONABLE a REASONABLE solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	27.4 Å
Skewness Skewness skewness	0.522
Kurtosis Kurtosis kurtosis	-0.632
Angular range angular_range	— – 0.2250 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	22050000.0000
Real-space data points n_real_points	46
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.402; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.384; Smooth: 0.817

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Description description	Ligninase H8
Molecular weight formula_weight	37441.7 kDa
EC 编号 ec_number	1.11.1.14
Mutation mutation	W171F SUBSTITUTION
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	5938

AAVIEKRATCSNGKTVGDASCCAWFDVLDDIQQNLFHGGQCGAEAHESIRLVFHDSIAISPAMEAQGKFGGGGADGSIMIFDDIETAFHPNIGLDEIVKLQKPFVQKHGVTPGDFIAFAGAVALSNCPGAPQMNFFTGRAPATQPAPDGLVPEPFHTVDQIINRVNDAGEFDELELVFMLSAHSVAAVNDVDPTVQGLPFDSTPGIFDSQFFVETQLRGTAFPGSGGNQGEVESPLPGEIRIQSDHTIARDSRTACEWQSFVNNQSKLVDDFQFIFLALTQLGQDPNAMTDCSDVIPQSKPIPGNLPFSFFPAGKTIKDVEQACAETPFPTLTTLPGPETSVQRIPPPPGA

来源 Source

来源生物 organism	Phanerochaete chrysosporium
通用名 common_name	White-rot fungus
NCBI Class编号 ncbi_taxonomy_id	5306
宿主生物 host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	CALCIUM ION
Molecular weight formula_weight	40.1 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 3 Entity 3 non-polymer

Description description	PROTOPORPHYRIN IX CONTAINING FE
Molecular weight formula_weight	616.5 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	636

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7. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d1b85a_
Class class	a — All alpha proteins
Fold Fold fold	a.93 — Heme-dependent peroxidases
Superfamily Superfamily superfamily	a.93.1 — Heme-dependent peroxidases
Family Family family	a.93.1.1 — CCP-like

Domain ID domain_id	d1b85b_
Class class	a — All alpha proteins
Fold Fold fold	a.93 — Heme-dependent peroxidases
Superfamily Superfamily superfamily	a.93.1 — Heme-dependent peroxidases
Family Family family	a.93.1.1 — CCP-like

CATH v4.4 (4 domains)

Domain ID domain_id	1b85A01
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	520 — Peroxidase; domain 1
Homologous superfamily homologous superfamily	10 —

Domain ID domain_id	1b85A02
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	420 — Peroxidase; domain 2
Homologous superfamily homologous superfamily	10 — Peroxidase, domain 2

Domain ID domain_id	1b85B01
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	520 — Peroxidase; domain 1
Homologous superfamily homologous superfamily	10 —

Domain ID domain_id	1b85B02
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	420 — Peroxidase; domain 2
Homologous superfamily homologous superfamily	10 — Peroxidase, domain 2

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8. Citations (3)

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Unit-cell length a length_a	73.400 Å
Unit-cell length b length_b	94.400 Å
Unit-cell length c length_c	230.990 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	16

Space group space_group	C 2 2 21
Space-group number int_tables_number	20
Crystal system crystal_system	—

Resolution resolution	1.850 Å
Low-resolution limit resolution_low	12.000 Å
R factor r_factor	—
R_work r_work	0.1420
R_free r_free	0.1810

fit	/app/data/saxs_computation/b8/1b85/1b85.fit
pddf	/app/data/pr_computation/b8/1b85/1b85.pr.out
profile	/app/data/saxs_computation/b8/1b85/1b85.dat

LIGNIN PEROXIDASE

1. Protein Identity and Related Structures Protein Identity & Related Structures

Ligninase H8

State in the Current Structure

Other States of the Same Protein in the Database

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

2. Structure Basics 2. Structure Basics

3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

5. Crystallography and Experiment 5. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction